OpenMS  3.0.0
FIAMSScheduler.h
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31 // $Maintainer: Svetlana Kutuzova, Douglas McCloskey $
32 // $Authors: Svetlana Kutuzova, Douglas McCloskey $
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34 
35 #pragma once
36 
37 #include <OpenMS/FORMAT/CsvFile.h>
38 #include <map>
39 
40 namespace OpenMS
41 {
42 class MzMLFile;
43 /*
44  @brief Scheduler for FIA-MS data batches. Works with FIAMSDataProcessor.
45 
46  The class is initialised with the path to the csv file that must contain the following columns:
47  - *filename* - the mzML filename for the sample. Must not contains the extension and path. The results filenames follow the pattern @filename_@n_seconds.
48  - *dir_input* - the location of the directory with the mzML file
49  - *dir_output* - the location of the directory where the results will be stored
50  - *resolution* - the resolution of the instrument
51  - *polarity* - the charge of the instrument, accepts "positive" or "negative"
52  - *db:mapping* - database input file containing three tab-separated columns of mass, formula, identifier for the accurate mass search
53  - *db:struct* - database input file containing four tab-separated columns of identifier, name, SMILES, INCHI for the accurate mass search
54  - *positive_adducts* - file containing the list of potential positive adducts for the accurate mass search
55  - *negative_adducts* - file containing the list of potential negative adducts for the accurate mass search
56  - *time* - ";"-separated numbers of seconds to process, f.e. "30;60;90;180"
57 */
58 class OPENMS_DLLAPI FIAMSScheduler
59  {
60 public:
61  FIAMSScheduler() = default;
62 
65  String filename,
66  String base_dir = "/",
67  bool load_cached_ = true
68  );
69 
71  ~FIAMSScheduler() = default;
72 
74  FIAMSScheduler(const FIAMSScheduler& cp) = default;
75 
77  FIAMSScheduler& operator=(const FIAMSScheduler& fdp) = default;
78 
82  void run();
83 
87  const std::vector<std::map<String, String>>& getSamples();
88 
92  const String& getBaseDir();
93 
94 private:
98  void loadSamples_();
99 
103  std::vector<std::map<String, String>> samples_;
104  };
105 } // namespace OpenMS
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FIAMSScheduler::load_cached_
bool load_cached_
Definition: FIAMSScheduler.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
CsvFile.h
OpenMS::FIAMSScheduler::samples_
std::vector< std::map< String, String > > samples_
Definition: FIAMSScheduler.h:103
OpenMS::FIAMSScheduler
Definition: FIAMSScheduler.h:58
OpenMS::FIAMSScheduler::filename_
String filename_
Definition: FIAMSScheduler.h:100
OpenMS::FIAMSScheduler::base_dir_
String base_dir_
Definition: FIAMSScheduler.h:101